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Add dbghaplo #51035

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merged 9 commits into from
Sep 30, 2024
Merged

Add dbghaplo #51035

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414d535
Added dbghaplo recipe.
bluenote-1577 Sep 30, 2024
6cb0d19
Added dbghaplo recipe v0.02
bluenote-1577 Sep 30, 2024
509d684
space between versioning issue
bluenote-1577 Sep 30, 2024
8c51acb
Changed lofreq command
bluenote-1577 Sep 30, 2024
08db56d
Update recipes/dbghaplo/meta.yaml
bluenote-1577 Sep 30, 2024
a193b14
Update recipes/dbghaplo/build.sh
bluenote-1577 Sep 30, 2024
d745937
Update recipes/dbghaplo/meta.yaml
bluenote-1577 Sep 30, 2024
1a302a1
Update recipes/dbghaplo/meta.yaml
bluenote-1577 Sep 30, 2024
de2c9f2
Update recipes/dbghaplo/meta.yaml
bluenote-1577 Sep 30, 2024
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9 changes: 9 additions & 0 deletions recipes/dbghaplo/build.sh
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Original file line number Diff line number Diff line change
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#!/bin/bash -euo

# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details.
# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo"

# build statically linked binary with Rust
RUST_BACKTRACE=1 cargo install --verbose --path . --root $PREFIX
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cp scripts/* $PREFIX/bin
48 changes: 48 additions & 0 deletions recipes/dbghaplo/meta.yaml
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{% set version="0.0.2" %}

package:
name: dbghaplo
version: {{ version }}

source:
url: https://github.com/bluenote-1577/dbghaplo/archive/v{{ version }}.tar.gz

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sha256: e7e2741afb0c7f12718ec969815d3c8f18ce7ba66517e21c6fcfb3fe4262780b

build:
number: 0
run_exports:
- {{ pin_subpackage('dbghaplo', max_pin="x.x") }}
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⚠️ Potential issue

Correction needed: Adjust pin_subpackage syntax.

The use of run_exports with pin_subpackage is good for ABI compatibility. However, the syntax for pin_subpackage is incorrect.

Please update the run_exports section as follows:

build:
  number: 0
  run_exports:
    - {{ pin_subpackage('dbghaplo', max_pin='x.x') }}

Note the single quotes around 'x.x' and the use of an equals sign instead of a colon.


requirements:
build:
- {{ compiler("cxx") }}
- rust >=1.70
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- make
- cmake >=3.12
run:
- python
- samtools
- minimap2
- lofreq >=2.1.5
- tabix
- pysam >=0.16
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🛠️ Refactor suggestion

Consider specifying Python version and adding version constraints for dependencies.

The requirements look good overall, but there are a few improvements to consider:

  1. It's recommended to specify the Python version to ensure compatibility. Consider adding a version constraint, e.g., python >=3.6.
  2. Add version constraints for samtools and minimap2 if specific versions are required.

Here's a suggested update to the run requirements:

  run:
    - python >=3.6
    - samtools >=1.9
    - minimap2 >=2.17
    - lofreq >=2.1.5
    - tabix
    - pysam >=0.16

Please adjust the Python version and other tool versions according to your package's specific requirements.


test:
commands:
- dbghaplo -h
- samtools --help
- minimap2 --help
- lofreq version
- tabix --help
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- run_dbghaplo_pipeline -h
- haplotag_bam -h
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about:
home: https://github.com/bluenote-1577/dbghaplo
license: MIT
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summary: Haplotyping small sequences from heterogeneous long-read sequencing samples with a SNP-encoded positional de Bruijn Graph.

extra:
recipe-maintainers:
- bluenote-1577